Genetic diversity and population structure of four Nigerian indigenous cattle breeds

E N Nwachukwu; D J U Kalla; H O Ukwu; C C Ogbu; J Ezea; U H Udoh; O O Ekumankama

doi:10.1007/s11250-022-03132-8

Genetic diversity and population structure of four Nigerian indigenous cattle breeds

Trop Anim Health Prod. 2022 Mar 8;54(2):132. doi: 10.1007/s11250-022-03132-8.

Authors

E N Nwachukwu¹, D J U Kalla², H O Ukwu³, C C Ogbu⁴, J Ezea¹, U H Udoh⁵, O O Ekumankama⁶

Affiliations

¹ Department of Animal Breeding and Physiology, Michael Okpara University of Agriculture, Umudike, Abia State, Nigeria.
² Department of Animal Production, Abubakar Tafawa Balewa University, Bauchi, Bauchi State, Nigeria.
³ Department of Animal Breeding and Physiology, Federal University of Agriculture, Makurdi, Benue State, Nigeria. ukwu.henry@uam.edu.ng.
⁴ Department of Veterinary Biochemistry and Animal Production, Michael Okpara University of Agriculture, Umudike, Abia State, Nigeria.
⁵ Department of Animal Science, University of Uyo, Uyo, Akwa Ibom State, Nigeria.
⁶ Department of Agricultural Extension and Rural Sociology, Michael Okpara University of Agriculture, Umudike, Abia State, Nigeria.

PMID: 35260931
DOI: 10.1007/s11250-022-03132-8

Abstract

A total of thirty-eight (38) Nigerian indigenous cattle were used to evaluate the genetic relatedness, diversity, and population structure of four indigenous cattle breeds. Blood samples were collected from the experimental animals into vacutainer tubes containing EDTA, and genomic DNA extracted, quantified, and evaluated for integrity. Fourteen (14) microsatellite primers were used for polymerase chain reaction (PCR) and PCR amplification performed under standard conditions followed by electrophoresis in 2.5% Metaphor Agarose gel. Genomic parameter estimates included allele number (Na), observed (H_o) and expected (H_e) heterozygosity, polymorphism information content (PIC), test of Hardy-Weinberg equilibrium, and genetic diversity; pairwise Nei's genetic distance, Wright's F-statistics (FIT, FST, and FIS), and gene flow (Nm); and breed relationship, population structure, and degree of admixture. A total of 112 alleles were detected and mean number of alleles was 4.02 ± 0.190, while mean fixation index was 0.461 ± 0.068. Mean H_o and H_e were 0.352 ± 0.05 and 0.605 ± 0.018, respectively. Pairwise estimates of genetic differentiation, F_ST, were significantly different (p < 0.001) implying distinct breeds. Estimates of Nm were less than 4 but greater than 1, indicating that the cattle breeds do not belong to one panmictic population. Estimates of pairwise genetic distance revealed that White Fulani and Sokoto Gudali were more closely related than Muturu and N'Dama. The results of STRUCTURE, principal coordinate, and phylogenetic analyses revealed four clusters which implies that the breeds were genetically distinct. It is recommended that the four cattle breeds can be used to develop composites with higher genetic potentials for beef production and resistance to endemic diseases and pests. Further efforts should be made to conserve and genetically improve these breeds to meet present and future production and breeding imperatives.

Keywords: Genetic diversity; Heterozygosity; Indigenous cattle; Microsatellite.

MeSH terms

Alleles
Animals
Cattle / genetics
Genetic Variation
Microsatellite Repeats*
Nigeria
Phylogeny
Polymorphism, Genetic*

Grants and funding

TETF/DR&D/CE/NRF/78/STI/VOL.1/Tertiary Education Trust Fund